Wrong octane-dirty little secret?

So, I got my '03 Accord EX not too long ago. This last weekend my hubby changed two of the engine mounts, and I discovered afterwards that the engine was running really, really rough. My first thought was that perhaps the vacuum hose under the center mount didn't seat all the way or came loose, because after driving the car back and forth to work a couple of times, I also discovered that it was burning more gas.
Our local mechanic took a look at it today, and his assessment was that I'm not using the correct grade fuel. He says it doesn't need a tune up and everything else looked okay. Since I typically put the ethanol blend gas in my vehicles, I didn't think much of it. However, he says I should be putting the higher octane fuel in (90 or higher) and it should fix things.
I looked in the owner's manual after he said this, and the book does say to use higher octane, but it recommended 86 or higher. What I normally use is 87, so I would think this should be okay. But that rating was done in 2003.

Is it really possible that using just the wrong octane rated fuel can cause my car to run rough and loud? When I bought the car 3 weeks ago, it had about a half tank of gas, and I filled it up then. Since then, I have put another full tank in.

Has anyone ever had this happen? If it is simply a matter of paying a little extra at each fill-up to keep my little Honda happy, I'm going to. But I don't want to assume that that's it, keep driving, and have the engine eat itself up into confetti. Help?

Did you figure out the problem?